Environment-Dependent Fitness Gains Can Be Driven by Horizontal Gene Transfer of Transporter-Encoding Genes
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Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes David S. Milnera,1, Victoria Attaha, Emily Cooka, Finlay Maguirea,b, Fiona R. Savorya, Mark Morrisona, Carolin A. Müllerc, Peter G. Fosterd, Nicholas J. Talbota,2, Guy Leonarda, and Thomas A. Richardsa,1 aBiosciences, Living Systems Institute, University of Exeter, EX4 4QD Exeter, United Kingdom; bFaculty of Computer Science, Dalhousie University, Halifax, B3H 4R2 NS, Canada; cThe Sir William Dunn School of Pathology, University of Oxford, OX1 3RE Oxford, United Kingdom; and dDepartment of Life Sciences, Natural History Museum, SW7 5BD London, United Kingdom Edited by Nancy A. Moran, University of Texas at Austin, Austin, TX, and approved January 28, 2019 (received for review September 19, 2018) Many microbes acquire metabolites in a “feeding” process where interactions (28–30). Furthermore, membrane transporter HGT complex polymers are broken down in the environment to their events in eukaryotes have been described previously (5, 19, 31, 32), subunits. The subsequent uptake of soluble metabolites by a cell, although relatively little work has been conducted to investigate sometimes called osmotrophy, is facilitated by transporter pro- the functional impact of HGT of transporter genes across fungal teins. As such, the diversification of osmotrophic microorganisms phyla and the subsequent consequences of gene acquisition on the is closely tied to the diversification of transporter functions. Hor- fitness of recipient lineages. This analysis would, in turn, allow the izontal gene transfer (HGT) has been suggested to produce genetic examination of how differing environmental conditions can dictate variation that can lead to adaptation, allowing lineages to acquire whether HGT-acquired genes are maintained by selection within traits and expand niche ranges. Transporter genes often encode lineages, informing our understanding of pan-genome evolution in single-gene phenotypes and tend to have low protein–protein in- eukaryotic microbes, such as fungi. teraction complexity and, as such, are potential candidates for Fungi are obligate osmotrophs and often perform a range of HGT. Here we test the idea that HGT has underpinned the expan- lysotrophic functions (33), feeding by secreting extracellular en- sion of metabolic potential and substrate utilization via transfer of zymes into the environment, degrading complex molecules, and transporter-encoding genes. Using phylogenomics, we identify importing the resulting nutrients into the cell (25). Transporter EVOLUTION seven cases of transporter-gene HGT between fungal phyla, and proteins are central to this process, allowing the uptake of simple investigate compatibility, localization, function, and fitness conse- monomers following extracellular enzymatic degradation. As such, quences when these genes are expressed in Saccharomyces cerevi- the gain (e.g., by HGT or duplication) and loss of transporter siae. Using this approach, we demonstrate that the transporters proteins in fungi is hypothesized to be a key evolutionary process identified can alter how fungi utilize a range of metabolites, includ- in driving niche range and influencing social interactions (25). We therefore sought to identify transporter gene HGT events ing peptides, polyols, and sugars. We then show, for one model in fungi, and examine the types of functional constraints such gene, that transporter gene acquisition by HGT can significantly HGTs must overcome to become fixed within a recipient line- alter the fitness landscape of S. cerevisiae. We therefore provide age. Here, we have identified seven instances of transporter evidence that transporter HGT occurs between fungi, alters how gene HGT between fungal phyla, characterized the function of fungi can acquire metabolites, and can drive gain in fitness. We each using phenotype microarrays or genetic complementation, propose a “transporter-gene acquisition ratchet,” where trans- porter repertoires are continually augmented by duplication, HGT, and differential loss, collectively acting to overwrite, fine-tune, and Significance diversify the complement of transporters present in a genome. Horizontal gene transfer (HGT) is the transfer of genetic in- lateral gene transfer | protein connectivity | osmotrophy | formation between genomes by a route other than from par- gene ratchet | fungi ent to offspring. Of particular interest here are the transfers of transporter-encoding genes, which can allow an organism to utilize a new metabolite, often via the acquisition of a single orizontal, or lateral, gene transfer (HGT) is the movement foreign gene. Here we have identified a range of HGT events of of genetic material between reproductively isolated ge- H transporter-encoding genes, characterized the substrate pref- nomes, and operates in contrast to vertical inheritance, where erences for each HGT encoded protein, and demonstrated that genes are passed from parent to progeny. HGT events are the gain of one of these HGTs can provide yeast with a distinct common in prokaryotes (1, 2) and, although less common, it is competitive advantage in a given environment. This has wide becoming apparent that HGT events into eukaryotes are a sig- implications for understanding how acquisition of single genes by nificant factor (3) and contribute toward the evolution of HGT can drastically influence the environments fungi can colonize. eukaryotic microbes, including oomycetes (4–8) and fungi (9–12). Previous work has demonstrated that HGT events in eukaryotes Author contributions: D.S.M., N.J.T., and T.A.R. designed research; D.S.M., V.A., E.C., produce genetic variation that can lead to adaptation, allowing M.M., and T.A.R. performed research; C.A.M. contributed new reagents/analytic tools; lineages to utilize alternative nutrients, colonize new environ- D.S.M., V.A., E.C., F.M., F.R.S., P.G.F., G.L., and T.A.R. analyzed data; and D.S.M., N.J.T., ments, and expand niche ranges (3, 10, 13–15). Furthermore, G.L., and T.A.R. wrote the paper. experimental characterization of the functions of horizontally ac- The authors declare no conflict of interest. quired gene products (12, 16–24) has reinforced the hypothesis This article is a PNAS Direct Submission. that HGT can drive adaptive potential in eukaryotes. This open access article is distributed under Creative Commons Attribution-NonCommercial- Transporter genes are potential candidates for acquisition by NoDerivatives License 4.0 (CC BY-NC-ND). HGT as they constitute single-gene phenotypes (i.e., a single 1To whom correspondence may be addressed. Email: [email protected] or t.a. gene that encodes an entire functional trait), with the proteins [email protected]. they encode tending to have low protein–protein interaction 2Present address: The Sainsbury Laboratory, Norwich Research Park, NR4 7UH Norwich, complexity (12, 25). Consistent with this hypothesis, previous United Kingdom. work has demonstrated that phenotypes can be acquired by This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. single-gene HGTs (e.g., refs. 23, 26, and 27), and that HGTs tend 1073/pnas.1815994116/-/DCSupplemental. to encode proteins that have a low number of protein–protein www.pnas.org/cgi/doi/10.1073/pnas.1815994116 PNAS Latest Articles | 1of10 Downloaded by guest on October 3, 2021 and examined the fitness effects of one model HGT event using transcriptional load. This was consistent with poor growth rate (r) heterologous expression in Saccharomyces cerevisiae. These results of the two strains (Fig. 2J and SI Appendix,Fig.S1), both of which show that single-gene transfer of transporter-encoding genes can had an r median value of <55% of the wild-type S. cerevisiae drive environment-dependent fitness traits, demonstrating that strain, containing only the empty p426-GPD vector. One reason gain and loss of “bolt-on-traits” can drive pan-genome evolution for such poor growth may be the unregulated uptake of toxic in fungi. levels of substrate into the cell. The uptake of large quantities of single amino acids, for example, has been shown to be toxic to S. Results and Discussion cerevisiae (38). Both HGT-2 and HGT-5 show homology to LysP Identification of Transporter HGTs Between Ascomycetes and amino acid permeases (Table 1), suggesting that altered amino Basidiomycetes. Using phylogenomic approaches we sought to acid uptake may be the cause of poor growth rate when expressed identify transporter proteins for which phylogenetic analysis iden- in S. cerevisiae, and demonstrating that transferred transporters tifies a tree topology consistent with recent HGT between the as- can be incompatible with foreign cellular environments, and thus comycetes and basidiomycetes. To identify candidate HGTs, we represent a potential barrier to transporter HGT in certain envi- generated a phylogeny for every protein annotated as a transporter ronment, genetic, and cellular contexts. in the S. cerevisiae S288c genome (34) using an automated pipeline Previous work has shown that functional HGTs tend to encode (35). Putative HGT phylogenies were identified as tree topologies proteins exhibiting a low number of protein–protein interactions that demonstrated genes from a closely related group, the recipient, (28–30). Furthermore, transporter proteins show similar levels of branching within a clade of distantly related taxa, the donor group protein–protein interaction complexity to previously identified (36). Amino acid sequence